Mercurial > repos > iuc > data_manager_snpsift_dbnsfp
changeset 5:09f9bfb2b33b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
| author | iuc |
|---|---|
| date | Tue, 30 Oct 2018 18:44:43 -0400 |
| parents | 47f276ffcbfc |
| children | e57f0b0bc73b |
| files | data_manager/data_manager_snpsift_dbnsfp.py tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/data_manager/data_manager_snpsift_dbnsfp.py Tue Apr 04 18:15:17 2017 -0400 +++ b/data_manager/data_manager_snpsift_dbnsfp.py Tue Oct 30 18:44:43 2018 -0400 @@ -43,7 +43,7 @@ softgenetics_url = 'ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/' dbNSFP_file_pat = '(dbNSFP(.*)_variant|dbscSNV(.*)).chr(.*)' tokenize = re.compile(r'(\d+)|(\D+)').findall -dbNSFP_name_pat = 'dbNSFP(v|_light)?(\d*).*?' +dbNSFP_name_pat = r'dbNSFP(v|_light)?(\d*).*?' def stop_err(msg): @@ -53,7 +53,7 @@ def get_nsfp_genome_version(name): genome_version = 'hg19' - dbNSFP_name_pat = '(dbscSNV|dbNSFP(v|_light)?)(\d*).*?' + dbNSFP_name_pat = r'(dbscSNV|dbNSFP(v|_light)?)(\d*).*?' m = re.match(dbNSFP_name_pat, name) if m: (base, mid, ver) = m.groups() @@ -167,7 +167,7 @@ bzip_path = None if options.softgenetics: dbnsfp_url = softgenetics_url + options.softgenetics - db_name = options.db_name if options.db_name else re.sub('\.zip$', '', options.softgenetics) + db_name = options.db_name if options.db_name else re.sub(r'\.zip$', '', options.softgenetics) genome_version = get_nsfp_genome_version(options.softgenetics) tsv = db_name + '.tsv' dbnsfp_tsv = download_dbnsfp_database(dbnsfp_url, tsv)
--- a/tool_dependencies.xml Tue Apr 04 18:15:17 2017 -0400 +++ b/tool_dependencies.xml Tue Oct 30 18:44:43 2018 -0400 @@ -1,6 +1,6 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <tool_dependency> <package name="pysam" version="0.8.3"> - <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file